eccD2 Family assigned · medium auto-curated
H37Rv Rv3887c · MTBC0 mtbc0_004121 ·
509 aa · 4394401–4395930 (-) ·
RefSeq NP_218404.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ESX-2 secretion system protein EccD |
|---|---|
| MTBC0 PGAP re-annotation | type VII secretion system ESX-2 subunit EccD2 |
| Revised (this work) | Type VII secretion system ESX-2 subunit EccD2. Pfam: YukD (PF08817.17), EccD (PF19053.7). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WNQ5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ESX-2 secretion system protein eccD2 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | eccD2 |
| eggNOG description | WXG100 protein secretion system (Wss), protein YukD |
| Orthologous group | 2B6TY |
| Gene Ontology (25) |
GO:0008150, GO:0009605, GO:0009607, GO:0020012, GO:0030682, GO:0042783, GO:0043207, GO:0044403, GO:0044413, GO:0044415, GO:0044419, GO:0050896 +13 more
|
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 1.059 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 17 missense, 0 nonsense, 6 frameshift |
| Disruption | 6 distinct premature-stop/frameshift site(s); most common in 0.63% of strains (922) · convergent |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
YukD | PF08817.17 | 1.2e-12 | 13–93 | WXG100 protein secretion system (Wss), protein YukD |
EccD | PF19053.7 | 6.6e-28 | 141–509 | EccD-like transmembrane domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mycP2 (membrane-anchored mycosin), high confidence from genomic context alone (score 952 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3886c mycP2 |
membrane-anchored mycosin | 952 | 952 ctx | neighborhood:881 cooccurence:531 |
Rv3888c |
membrane protein | 993 | 949 ctx | neighborhood:881 cooccurence:568 textmining:870 |
Rv3884c eccA2 |
ESX-2 secretion system protein EccA | 916 | 899 ctx | neighborhood:794 cooccurence:519 |
Rv3885c eccE2 |
ESX-2 secretion system protein EccE | 884 | 885 ctx | neighborhood:881 |
Rv3899c hyp |
hypothetical protein | 879 | 880 ctx | cooccurence:772 coexpression:430 |
Rv3894c eccC2 |
ESX-2 type VII secretion system protein EccC | 880 | 876 ctx | cooccurence:762 |
Rv3895c eccB2 |
ESX-2 secretion system protein EccB | 851 | 828 ctx | cooccurence:764 |
Rv1782 eccB5 |
ESX-5 type VII secretion system protein EccB5 | 824 | 788 ctx | cooccurence:734 |
Rv1783 eccC5 |
ESX-5 type VII secretion system protein EccC5 | 877 | 781 ctx | cooccurence:637 textmining:462 |
Rv2423 hyp |
hypothetical protein | 747 | 747 ctx | cooccurence:747 |
Rv0256c PPE2 |
PPE family protein PPE2 | 712 | 713 ctx | cooccurence:711 |
Rv2067c hyp |
hypothetical protein | 708 | 709 ctx | cooccurence:707 |
Rv1796 mycP5 |
membrane-anchored mycosin MycP | 698 | 697 ctx | cooccurence:676 |
Rv2082 hyp |
hypothetical protein | 678 | 679 ctx | cooccurence:441 coexpression:446 |
Rv3446c hyp |
hypothetical protein | 672 | 672 ctx | cooccurence:661 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Legacy H37Rv annotation: ESX-2 secretion system protein EccD
- MTBC0 PGAP product: type VII secretion system ESX-2 subunit EccD2
- Pfam (hmmscan --cut_ga): YukD PF08817.17 (E=1e-12), EccD PF19053.7 (E=7e-28)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_218404.1)
- Domains: Pfam-A via hmmscan --cut_ga — YukD (PF08817.17), EccD (PF19053.7)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
2B6TY - Curated reference: UniProt P9WNQ5 (SwissProt, reviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
61 functional partner(s); context anchor
mycP2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004121|Rv3887c|eccD2 MTAPHKVAFPARCAVNICYDKHLCSQVFPAGIPVEGFFEGMVELFDADLKRKGFDGVALPAGSYELHKINGVRLDINKSLDELGVQDGDTLVLVPRVAGESFEPQYESLSTGLAAMGKWLGRDGGDRMFAPVTSLTAAHTAMAIIAMAVGVVLALTLRTRTITDSPVPAAMAGGIGVLLVIGALVVWWGWRERRDLFSGFGWLAVVLLAVAAACAPPGALGAAHALIGLVVVVLGAITIGVATRKRWQTAVVTAVVTVCGILAAVAAVRMFRPVSMQVLAICVLVGLLVLIRMTPTVALWVARVRPPHFGSITGRDLFARRAGMPVDTVAPVSEADADDEDNELTDITARGTAIAASARLVNAVQVGMCVGVSLVLPAAVWGVLTPRQPWAWLALLVAGLTVGLFITQGRGFAAKYQAVALVCGASAAVCAGVLKYALDTPKGVQTGLLWPAIFVAAFAALGLAVALVVPATRFRPIIRLTVEWLEVLAMIALLPAAAALGGLFAWLRH